Successful genomic and pathway engineering requires that metabolic flux be increased through select pathways, while not substantially interfering with viability and/or growth of the organism, or a desired phenotype. This can be especially pertinent for substrates or intermediates of the desired pathway that are involved in core or primary metabolism, or for branch intermediates involved in more than one pathway. Stephanopoulos, Metabolic Fluxes and Metabolic Engineering, Metabolic Engineering 1, 1-11 (1999). In fact, genetic alterations, or combinations of genetic alterations, that increase metabolic flux through a desired pathway are difficult to predict, limiting the usefulness of rational engineering approaches. Kern A, et al., Engineering primary metabolic pathways of industrial microorganisms, J. Biotechnology 129: 6-29 (2007). Further, it is often impractical to generate random and discrete mutational events in vivo and screen or select for improved metabolic flux or biomolecular function.
Methods are needed for screening the genetic space of a host organism to identify changes in endogenous genes and/or heterologous recombinant genes that provide improved phenotypes, such as in metabolic flux and balance, so as to improve or optimize microbial processes, including production of desired chemicals and biomolecules at industrial levels, or bioremediation applications.